According to the official government news agency Radiobras, a report by the president's Special Secretariat for Human Rights found at least two of 19 alleged drug traffickers killed in the raid on the Alemao slum were shot in the head at close range while lying face down on the ground.
Rio de Janeiro State Security Secretary Jose Mariano Beltrame attacked the report as baseless and "made to order, under pressure, from those who would smear the good cause of human rights," in an e-mail to the O Globo newspaper.
Because of the Day of the Dead holiday in Brazil, no one was available either at the security secretariat or human rights secretariat to comment on the report.
The June 27 raid on the Alemao shantytown complex involved 1,350 officers and capped two months of battles between police and drug gangs that claimed 38 lives and wounded 70 people. The battles were sparked by the killing of two police officers in May.
The raid was widely seen as a show of force by police to clamp down on the heavily armed drug gangs that rule most of this city's over 600 shantytowns before the start of a regional, Olympics-like athletic competition in Rio.
The federal report released late Thursday night found evidence of summary executions, citing the "large number of bullet holes entering from the backs of the bodies, numerous injuries in lethal regions, the volume of shots per victim, the proximity of the shots, and the lack of reports of attempts to capture the victims and the lack of defensive conduct on the part of the victims."
The report found that two men, Jose da Silva Farias Junior and Emerson Goulart, were killed with an initial shot at close range to the cranium passing from the back of the head to the front.
Recent police raids in Rio enjoy the widespread support among Rio residents.
But human rights groups and many security experts question their efficacy. They point out that the police quickly leave, returning control of the slums to drug gangs.